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- EMDB-54022: Agrobacterium phage 7-7-1 tail spike -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54022
TitleAgrobacterium phage 7-7-1 tail spike
Map dataAgrobacterium 7-7-1 tail
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Putative tail fiber
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Tail spike / VIRUS
Function / homology
Function and homology information


biological process involved in interaction with host / hydrolase activity, hydrolyzing O-glycosyl compounds / viral life cycle / virion component / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Domain of unknown function DUF1565 / Protein of unknown function (DUF1565) / Carbohydrate-binding module superfamily 5/12 / Pectin lyase fold / Pectin lyase fold/virulence factor / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative tail fiber / Structural protein / Structural protein
Similarity search - Component
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsNoteborn WEM / Hoeksma T / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: To Be Published
Title: Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1
Authors: Noteborn WEM / Hoeksma T / Briegel A
History
DepositionJun 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54022.png

Downloads & links

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Map

FileDownload / File: emd_54022.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAgrobacterium 7-7-1 tail
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.299
Minimum - Maximum-0.94063497 - 1.9152651
Average (Standard dev.)0.0012558528 (±0.0657844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 767.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54022_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Agrobacterium 7-7-1 tail

Fileemd_54022_half_map_1.map
AnnotationAgrobacterium 7-7-1 tail
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Agrobacterium 7-7-1 tail

Fileemd_54022_half_map_2.map
AnnotationAgrobacterium 7-7-1 tail
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Agrobacterium phage 7-7-1

EntireName: Agrobacterium phage 7-7-1 (virus)
Components
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Putative tail fiber

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Supramolecule #1: Agrobacterium phage 7-7-1

SupramoleculeName: Agrobacterium phage 7-7-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1161931 / Sci species name: Agrobacterium phage 7-7-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 14.263938 KDa
SequenceString:
MAIRFHPTNA ALVACNAVVD LFDAGGSIEV YTGPQPNDPT VAVSTQTLLV TFAIPAPGYG PAELVPGQNY VRAPGALPAV AVPGASGVA AWARVKNNAG DVIFDGDVGT SASSAFVRLS TTNLTAGVGV SVTASEYRQP TR

UniProtKB: Structural protein

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Macromolecule #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 31.435197 KDa
SequenceString: MAGIFFSGGL PCTLTVNAAC GIETTGDDCP ALYYPPKCNV SVEPLQMNAI ISEIANAINA FGDLYDCSRL DNLKAALQKA RSICDLPPF ADAPDLDDRI AGCFDNTSST ITVQQLVNLV LSQAGGLCDL PQAGGIGDND LIAGCIGGAE ALVSLSTLRG A LGGGSISG ...String:
MAGIFFSGGL PCTLTVNAAC GIETTGDDCP ALYYPPKCNV SVEPLQMNAI ISEIANAINA FGDLYDCSRL DNLKAALQKA RSICDLPPF ADAPDLDDRI AGCFDNTSST ITVQQLVNLV LSQAGGLCDL PQAGGIGDND LIAGCIGGAE ALVSLSTLRG A LGGGSISG IIPQEVLFDQ WRAGGNWEVS QSTQNRTGFI VRSLKEGIGI TVSDLFVATG NGGYQSISQW EATTFLYETD AE GTSIDGG RQQAIAIVFK RGTQWYTKSG DVILPLGSDD GVIRFRTPGY QRLTIWSGAQ L

UniProtKB: Structural protein

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Macromolecule #3: Putative tail fiber

MacromoleculeName: Putative tail fiber / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 61.552719 KDa
SequenceString: MVLRPVLVGG LPGCVNLPSN DDCQCWPLWS SDNAYSFGDV VQQGGVLYTA NRDIPPGTPF LAGDWTVYTP GATLVPPHRE DASYQQYQA VNFNDKLYTA RTDLPPGPFD PANWQEISVE GLVEVADSST IDFSGDGSAS DPLTAAVKLD PVAGNLITAT P DGLVLLAS ...String:
MVLRPVLVGG LPGCVNLPSN DDCQCWPLWS SDNAYSFGDV VQQGGVLYTA NRDIPPGTPF LAGDWTVYTP GATLVPPHRE DASYQQYQA VNFNDKLYTA RTDLPPGPFD PANWQEISVE GLVEVADSST IDFSGDGSAS DPLTAAVKLD PVAGNLITAT P DGLVLLAS GIPFPDPSSV NISDNVTLRV DEVTGDDATA DGSLQKPYKT IVAAIGASNA GDNIEVYPGS YAGNFAPKSD TT VTGRGFV YVDGNVTIGA AVSGVTVSGL FIDGNLTIAG ANGTVEFINT TVSTSIIGTG NNTGWFLFDE VNADSVSITG AGT GEFIFR GGIEQTDFSL NAPSKLLVEN RSRVGVVNHL NGLMILKDIG VIVSLTSTAE DNAFTFLAVI SSSLFDPDPR TYGA LTKTG SCSYAFQDFA RSNMAETVTG AKWLVSNGRD IHGNYDPNFY ALPNGQSLNS HFEGIDNALQ TLQEYSPLGR SVAVD FGFS IIGGWSADET VGVHAVSHET VIPSNMAGSI MVTDSSTLDG VLNVMVGTSV VGTVTITDGA AVFASSEFNL DPGQLV RIV STSEGTFEYV GLTLVGHRQV VYVD

UniProtKB: Putative tail fiber

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 48966
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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